UPDATE:
Had my friend who is an ASE Master Tech stop by to do a compression test and help me check everything out. Even replaced another coil, regapped plugs, and cleaned everything... And there was the problem. Two weeks after changing plugs they were all again, along with the CPs oil covered. As soon as he removed the first CP he said he knew the problem (the Audi dealership several hundred dollars and days later apparently could not determine it). He said the spark plug tube seals were leaking.
As the oil got into the plugs it was causing the missing experienced mostly at startup and running thereafter. We cleaned everything and sure enough it started and ran fine yesterday with no codes, but this morning, it was all back with a vengeance. FYI, we went ahead and did the compression test and it was fine.
Contacting the dealer now (140 miles away). After paying them nearly $150 directly it incorrectly diagnose plugs as the issue plus the several hundred on a rental, gas, not having my car for days, parts, etc I expect to not have to pay a dime in this matter and probably a refund would be in order as well. I can only suggest they have it hauled in, fix it, and have it hauled back. They could have avoided that by fixing the actual issue while it sat on their lot....
I am quite displeased at this point....
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